Package etomica.molecule

Class MoleculeAgentManager<E>

java.lang.Object

etomica.molecule.MoleculeAgentManager<E>

Type Parameters:

E - molecule agent class

All Implemented Interfaces:

BoxEventListener

public final class MoleculeAgentManager<E>
extends java.lang.Object
implements BoxEventListener

MoleculeAgentManager acts on behalf of client classes (an AgentSource) to manage agents in every IMolecule in a box. When molecules are added or removed from the box, the agents array is updated.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	MoleculeAgentManager.MoleculeAgentSource<E>	Interface for an object that wants an agent associated with each IMolecule a Box.

Constructor Summary

Constructors

Constructor	Description
MoleculeAgentManager(Simulation sim, Box box, MoleculeAgentManager.MoleculeAgentSource<E> source)
MoleculeAgentManager(Simulation sim, Box box, java.util.function.Function<IMolecule,? extends E> agentSource)
MoleculeAgentManager(Simulation sim, Box box, java.util.function.Function<IMolecule,? extends E> agentSource, java.util.function.BiConsumer<? super E,IMolecule> onRelease)

Method Summary

Modifier and Type	Method	Description
java.util.stream.Stream<E>	agentStream()
void	boxMoleculeAdded(BoxMoleculeEvent e)	Called when a molecule is added to the box.
void	boxMoleculeIndexChanged(BoxMoleculeIndexEvent e)	Called when an molecule's index has changed.
void	boxMoleculeRemoved(BoxMoleculeEvent e)	Called when a molecule is removed from the box.
void	dispose()	Notifies the AtomAgentManager it should disconnect itself as a listener.
E	getAgent(IMolecule a)	Returns the agent associated with the given IAtom.
java.util.Map<ISpecies,IndexMap<E>>	getAgents()
Box	getBox()	Convenience method to return the box the Manager is tracking.
void	setAgent(IMolecule a, E newAgent)	Sets the agent associated with the given atom to be the given agent.

Methods inherited from interface etomica.box.BoxEventListener

boxAtomLeafIndexChanged, boxGlobalAtomLeafIndexChanged, boxNumberMolecules

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MoleculeAgentManager

public MoleculeAgentManager(Simulation sim,
                            Box box,
                            MoleculeAgentManager.MoleculeAgentSource<E> source)

MoleculeAgentManager

public MoleculeAgentManager(Simulation sim,
                            Box box,
                            java.util.function.Function<IMolecule,? extends E> agentSource)

MoleculeAgentManager

public MoleculeAgentManager(Simulation sim,
                            Box box,
                            java.util.function.Function<IMolecule,? extends E> agentSource,
                            java.util.function.BiConsumer<? super E,IMolecule> onRelease)

Method Detail

getAgents

public java.util.Map<ISpecies,IndexMap<E>> getAgents()

agentStream

public java.util.stream.Stream<E> agentStream()

getAgent

public E getAgent(IMolecule a)

Returns the agent associated with the given IAtom. The IAtom must be from the Box associated with this instance.

setAgent

public void setAgent(IMolecule a,
                     E newAgent)

Sets the agent associated with the given atom to be the given agent. The IAtom must be from the Box associated with this instance. The IAtom's old agent is not released. This should be done manually if needed.

getBox

public Box getBox()

Convenience method to return the box the Manager is tracking.

dispose

public void dispose()

Notifies the AtomAgentManager it should disconnect itself as a listener.

boxMoleculeAdded

public void boxMoleculeAdded(BoxMoleculeEvent e)

Description copied from interface: BoxEventListener

Called when a molecule is added to the box.

Specified by:

boxMoleculeAdded in interface BoxEventListener

Parameters:

e - the event, which contains the added molecule and the box to which it was added.

boxMoleculeRemoved

public void boxMoleculeRemoved(BoxMoleculeEvent e)

Description copied from interface: BoxEventListener

Called when a molecule is removed from the box.

Specified by:

boxMoleculeRemoved in interface BoxEventListener

Parameters:

e - the event, which contains the removed molecule and the box from which it was removed.

boxMoleculeIndexChanged

public void boxMoleculeIndexChanged(BoxMoleculeIndexEvent e)

Description copied from interface: BoxEventListener

Called when an molecule's index has changed. This typically happens after one molecule is removed and the indices of another molecule is changed to fill in the gap.

Specified by:

boxMoleculeIndexChanged in interface BoxEventListener

Parameters:

e - the event, which contains the box, the molecule whose index changed and the molecule's old index. The molecule's new index can be obtained from the atom.